[med-svn] [python-pysam] branch upstream updated (6528922 -> dadf905)

[Afif Elghraoui]

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afif pushed a change to branch upstream
in repository python-pysam.

      from  6528922   Imported Upstream version 0.9.1.4+ds
       new  dadf905   Imported Upstream version 0.10.0+ds

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 .travis.yml                                        |    4 +-
 bcftools/vcfisec.c                                 |    2 +-
 bcftools/vcfisec.c.pysam.c                         |    2 +-
 benchmark/cython_flagstat.py                       |   23 +
 benchmark/python_flagstat.py                       |   23 +
 buildwheels.sh                                     |   69 +
 cy_build.py                                        |    2 -
 doc/api.rst                                        |    2 +-
 doc/release.rst                                    |   29 +
 doc/usage.rst                                      |   14 +-
 pysam/__init__.py                                  |   77 +-
 pysam/chtslib.pyx                                  |   19 -
 ...{calignedsegment.pxd => libcalignedsegment.pxd} |    4 +-
 ...{calignedsegment.pyx => libcalignedsegment.pyx} |   88 +-
 .../{calignmentfile.pxd => libcalignmentfile.pxd}  |   40 +-
 .../{calignmentfile.pyx => libcalignmentfile.pyx}  |  343 ++---
 pysam/{cbcf.pxd => libcbcf.pxd}                    |   33 +-
 pysam/{cbcf.pyx => libcbcf.pyx}                    | 1505 +++++++++++---------
 pysam/libcbgzf.pyx                                 |  209 +++
 pysam/{cfaidx.pxd => libcfaidx.pxd}                |    4 +-
 pysam/{cfaidx.pyx => libcfaidx.pyx}                |   13 +-
 pysam/{chtslib.pxd => libchtslib.pxd}              |   18 +
 pysam/libchtslib.pyx                               |  265 ++++
 pysam/{csamfile.pxd => libcsamfile.pxd}            |    4 +-
 pysam/{csamfile.pyx => libcsamfile.pyx}            |    2 +-
 pysam/{ctabix.pxd => libctabix.pxd}                |   28 +-
 pysam/{ctabix.pyx => libctabix.pyx}                |   94 +-
 pysam/{ctabixproxies.pxd => libctabixproxies.pxd}  |    0
 pysam/{ctabixproxies.pyx => libctabixproxies.pyx}  |    4 +-
 pysam/{cutils.pxd => libcutils.pxd}                |    0
 pysam/{cutils.pyx => libcutils.pyx}                |   44 +-
 pysam/{cvcf.pxd => libcvcf.pxd}                    |    0
 pysam/{cvcf.pyx => libcvcf.pyx}                    |   12 +-
 pysam/utils.py                                     |    2 +-
 pysam/version.py                                   |    6 +-
 requirements.txt                                   |    2 +-
 run_tests_travis.sh                                |   82 +-
 samtools/sam_view.c.pysam.c                        |    4 +-
 setup.py                                           |   76 +-
 tests/AlignedSegment_test.py                       |   39 +-
 tests/AlignmentFile_test.py                        |  130 +-
 tests/SamFile_test.py                              |   12 +-
 tests/StreamFiledescriptors_test.py                |   82 ++
 tests/VariantFile_test.py                          |   80 +-
 tests/_compile_test.pyx                            |    4 +-
 tests/_cython_flagstat.pyx                         |    6 +-
 tests/cython_flagstat.py                           |   11 -
 tests/pysam_data/Makefile                          |    8 +-
 tests/pysam_data/ex3.sam                           |    4 +-
 tests/pysam_data/ex_spliced.sam                    |  297 ++++
 tests/python_flagstat.py                           |   11 -
 tests/samtools_test.py                             |    1 +
 52 files changed, 2539 insertions(+), 1294 deletions(-)
 create mode 100644 benchmark/cython_flagstat.py
 create mode 100644 benchmark/python_flagstat.py
 create mode 100755 buildwheels.sh
 delete mode 100644 pysam/chtslib.pyx
 rename pysam/{calignedsegment.pxd => libcalignedsegment.pxd} (97%)
 rename pysam/{calignedsegment.pyx => libcalignedsegment.pyx} (97%)
 rename pysam/{calignmentfile.pxd => libcalignmentfile.pxd} (83%)
 rename pysam/{calignmentfile.pyx => libcalignmentfile.pyx} (92%)
 rename pysam/{cbcf.pxd => libcbcf.pxd} (72%)
 rename pysam/{cbcf.pyx => libcbcf.pyx} (76%)
 create mode 100644 pysam/libcbgzf.pyx
 rename pysam/{cfaidx.pxd => libcfaidx.pxd} (94%)
 rename pysam/{cfaidx.pyx => libcfaidx.pyx} (97%)
 rename pysam/{chtslib.pxd => libchtslib.pxd} (99%)
 create mode 100644 pysam/libchtslib.pyx
 rename pysam/{csamfile.pxd => libcsamfile.pxd} (93%)
 rename pysam/{csamfile.pyx => libcsamfile.pyx} (92%)
 rename pysam/{ctabix.pxd => libctabix.pxd} (89%)
 rename pysam/{ctabix.pyx => libctabix.pyx} (94%)
 rename pysam/{ctabixproxies.pxd => libctabixproxies.pxd} (100%)
 rename pysam/{ctabixproxies.pyx => libctabixproxies.pyx} (99%)
 rename pysam/{cutils.pxd => libcutils.pxd} (100%)
 rename pysam/{cutils.pyx => libcutils.pyx} (92%)
 rename pysam/{cvcf.pxd => libcvcf.pxd} (100%)
 rename pysam/{cvcf.pyx => libcvcf.pyx} (99%)
 create mode 100644 tests/StreamFiledescriptors_test.py
 delete mode 100644 tests/cython_flagstat.py
 create mode 100644 tests/pysam_data/ex_spliced.sam
 delete mode 100644 tests/python_flagstat.py

-- 
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